My husband and I just completed Athens Istanbul cruise.
We booked most of our excursions independently and used the following operators:
Athens - we used Spiros from www.athenstaxi.net
He is very reasonable...around 200 euro for up to 4 people for a full day tour.
Istanbul & Kusadasi (Ephesus) - We used Byzance. E-mail is firstname.lastname@example.org
I found them very courteous, professional, and very quick to respond to my emails. There are many wonderful reviews about this company. They were first class and the guides were helpful, informative and very flexible.
Our favorite port was Santorini! We took the half day tour and still had time to shop and make it back to the ship for a late lunch. Everyone takes either the gondola or the donkies back down to the tenders! Fun!
Make sure to be out on deck when you sail into Malta! Nothing like it! We took a taxi into town and went to St. John's Co-cathedral. An amazing, pleasant surprise and right in the middle of town right above where the ship docks. Still had time to shop a bit and get back to the ship in time for lunch. (This always helps in the finance department!)
Mykonos, we didn't take a tour because the ship has a shuttle bus to town. We enjoyed the photo opportunities here as well as shopping for music. We heard some complaints from people who paid for tours here... but then there are always some unhappy campers everywhere!
We couldn't find anything to complain about the cruise. The price was right, the accommodations (ship and hotels) were great and the crew were very pleasant. We have no regrets (other than we aren't doing it again this year!!!).